EXACT2: the semantics of biomedical protocols

© 2014 Soldatova et al.; licensee BioMed Central. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.This article has been made available through the Brunel Open Access Publishing Fund.Background: The reliability and reproducibility of experimental procedures is a cornerstone of scientific practice. There is a pressing technological need for the better representation of biomedical protocols to enable other agents (human or machine) to better reproduce results. A framework that ensures that all information required for the replication of experimental protocols is essential to achieve reproducibility. Methods: We have developed the ontology EXACT2 (EXperimental ACTions) that is designed to capture the full semantics of biomedical protocols required for their reproducibility. To construct EXACT2 we manually inspected hundreds of published and commercial biomedical protocols from several areas of biomedicine. After establishing a clear pattern for extracting the required information we utilized text-mining tools to translate the protocols into a machine amenable format. We have verified the utility of EXACT2 through the successful processing of previously ‘unseen’ (not used for the construction of EXACT2) protocols. Results: The paper reports on a fundamentally new version EXACT2 that supports the semantically-defined representation of biomedical protocols. The ability of EXACT2 to capture the semantics of biomedical procedures was verified through a text mining use case. In this EXACT2 is used as a reference model for text mining tools to identify terms pertinent to experimental actions, and their properties, in biomedical protocols expressed in natural language. An EXACT2-based framework for the translation of biomedical protocols to a machine amenable format is proposed. Conclusions: The EXACT2 ontology is sufficient to record, in a machine processable form, the essential information about biomedical protocols. EXACT2 defines explicit semantics of experimental actions, and can be used by various computer applications. It can serve as a reference model for for the translation of biomedical protocols in natural language into a semantically-defined format.This work has been partially funded by the Brunel University BRIEF award and a grant from Occams Resources

An ontology to standardize research output of nutritional epidemiology : from paper-based standards to linked content

Background: The use of linked data in the Semantic Web is a promising approach to add value to nutrition research. An ontology, which defines the logical relationships between well-defined taxonomic terms, enables linking and harmonizing research output. To enable the description of domain-specific output in nutritional epidemiology, we propose the Ontology for Nutritional Epidemiology (ONE) according to authoritative guidance for nutritional epidemiology. Methods: Firstly, a scoping review was conducted to identify existing ontology terms for reuse in ONE. Secondly, existing data standards and reporting guidelines for nutritional epidemiology were converted into an ontology. The terms used in the standards were summarized and listed separately in a taxonomic hierarchy. Thirdly, the ontologies of the nutritional epidemiologic standards, reporting guidelines, and the core concepts were gathered in ONE. Three case studies were included to illustrate potential applications: (i) annotation of existing manuscripts and data, (ii) ontology-based inference, and (iii) estimation of reporting completeness in a sample of nine manuscripts. Results: Ontologies for food and nutrition (n = 37), disease and specific population (n = 100), data description (n = 21), research description (n = 35), and supplementary (meta) data description (n = 44) were reviewed and listed. ONE consists of 339 classes: 79 new classes to describe data and 24 new classes to describe the content of manuscripts. Conclusion: ONE is a resource to automate data integration, searching, and browsing, and can be used to assess reporting completeness in nutritional epidemiology

An Annotated Corpus for Machine Reading of Instructions in Wet Lab Protocols

We describe an effort to annotate a corpus of natural language instructions consisting of 622 wet lab protocols to facilitate automatic or semi-automatic conversion of protocols into a machine-readable format and benefit biological research. Experimental results demonstrate the utility of our corpus for developing machine learning approaches to shallow semantic parsing of instructional texts. We make our annotated Wet Lab Protocol Corpus available to the research community

Ontology-assisted database integration to support natural language processing and biomedical data-mining

Successful biomedical data mining and information extraction require a complete picture of biological phenomena such as genes, biological processes, and diseases; as these exist on different levels of granularity. To realize this goal, several freely available heterogeneous databases as well as proprietary structured datasets have to be integrated into a single global customizable scheme. We will present a tool to integrate different biological data sources by mapping them to a proprietary biomedical ontology that has been developed for the purposes of making computers understand medical natural language

Image database system for glaucoma diagnosis support

Tato práce popisuje přehled standardních a pokročilých metod používaných k diagnose glaukomu v ranném stádiu. Na základě teoretických poznatků je implementován internetově orientovaný informační systém pro oční lékaře, který má tři hlavní cíle. Prvním cílem je možnost sdílení osobních dat konkrétního pacienta bez nutnosti posílat tato data internetem. Druhým cílem je vytvořit účet pacienta založený na kompletním očním vyšetření. Posledním cílem je aplikovat algoritmus pro registraci intenzitního a barevného fundus obrazu a na jeho základě vytvořit internetově orientovanou tři-dimenzionální vizualizaci optického disku. Tato práce je součásti DAAD spolupráce mezi Ústavem Biomedicínského Inženýrství, Vysokého Učení Technického v Brně, Oční klinikou v Erlangenu a Ústavem Informačních Technologií, Friedrich-Alexander University, Erlangen-Nurnberg.This master thesis describes a conception of standard and advanced eye examination methods used for glaucoma diagnosis in its early stage. According to the theoretical knowledge, a web based information system for ophthalmologists with three main aims is implemented. The first aim is the possibility to share medical data of a concrete patient without sending his personal data through the Internet. The second aim is to create a patient account based on a complete eye examination procedure. The last aim is to improve the HRT diagnostic method with an image registration algorithm for the fundus and intensity images and create an optic nerve head web based 3D visualization. This master thesis is a part of project based on DAAD co-operation between Department of Biomedical Engineering, Brno University of Technology, Eye Clinic in Erlangen and Department of Computer Science, Friedrich-Alexander University, Erlangen-Nurnberg.

Stand-alone wearable system for ubiquitous real-time monitoring of muscle activation potentials

Wearable technology is attracting most attention in healthcare for the acquisition of physiological signals. We propose a stand-alone wearable surface ElectroMyoGraphy (sEMG) system for monitoring the muscle activity in real time. With respect to other wearable sEMG devices, the proposed system includes circuits for detecting the muscle activation potentials and it embeds the complete real-time data processing, without using any external device. The system is optimized with respect to power consumption, with a measured battery life that allows for monitoring the activity during the day. Thanks to its compactness and energy autonomy, it can be used outdoor and it provides a pathway to valuable diagnostic data sets for patients during their own day-life. Our system has performances that are comparable to state-of-art wired equipment in the detection of muscle contractions with the advantage of being wearable, compact, and ubiquitous

Evidences of spin-temperature in Dynamic Nuclear Polarization: an exact computation of the EPR spectrum

In dynamic nuclear polarization (DNP) experiments, the compound is driven out-of-equilibrium by microwave (MW) irradiation of the radical electron spins. Their stationary state has been recently probed via electron double resonance (ELDOR) techniques showing, at low temperature, a broad depolarization of the electron paramagnetic resonance (EPR) spectrum under microwave irradiation. In this theoretical manuscript, we develop a numerical method to compute exactly the EPR spectrum in presence of dipolar interactions. Our results reproduce the observed broad depolarisation and provide a microscopic justification for spectral diffusion mechanism. We show the validity of the spin-temperature approach for typical radical concentration used in dissolution DNP protocols. In particular once the interactions are properly taken into account, the spin-temperature is consistent with the non-monotonic behavior of the EPR spectrum with a wide minimum around the irradiated frequency.Comment: 8 pages, 7 figures. Title and abstract change

Smart vest for respiratory rate monitoring of COPD patients based on non-contact capacitive sensing

In this paper, a first approach to the design of a portable device for non-contact monitoring of respiratory rate by capacitive sensing is presented. The sensing system is integrated into a smart vest for an untethered, low-cost and comfortable breathing monitoring of Chronic Obstructive Pulmonary Disease (COPD) patients during the rest period between respiratory rehabilitation exercises at home. To provide an extensible solution to the remote monitoring using this sensor and other devices, the design and preliminary development of an e-Health platform based on the Internet of Medical Things (IoMT) paradigm is also presented. In order to validate the proposed solution, two quasi-experimental studies have been developed, comparing the estimations with respect to the golden standard. In a first study with healthy subjects, the mean value of the respiratory rate error, the standard deviation of the error and the correlation coefficient were 0.01 breaths per minute (bpm), 0.97 bpm and 0.995 (p < 0.00001), respectively. In a second study with COPD patients, the values were -0.14 bpm, 0.28 bpm and 0.9988 (p < 0.0000001), respectively. The results for the rest period show the technical and functional feasibility of the prototype and serve as a preliminary validation of the device for respiratory rate monitoring of patients with COPD.Ministerio de Ciencia e Innovación PI15/00306Ministerio de Ciencia e Innovación DTS15/00195Junta de Andalucía PI-0010-2013Junta de Andalucía PI-0041-2014Junta de Andalucía PIN-0394-201